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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $species_info = array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ) $local_species = 'sci' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $species_info = array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ) $local_species = 'sci' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ), 'gf_id' => 'HOM05D001111', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001111' ), 'data_identifier' => 'HOM05D001111', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001111', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '551', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p16510' => 'bna', 'A02p35670' => 'bna', 'A04p13270' => 'bna', 'A06p29550' => 'bna', 'A06p40830' => 'bna', 'A07p36790' => 'bna', 'A09p07840' => 'bna', 'A09p41100' => 'bna', 'Aa31LG11G910' => 'aar', 'Aa31LG2G4860' => 'aar', 'Aa31LG4G10520' => 'aar', 'Aa31LG7G7610' => 'aar', 'Actinidia08163' => 'ach', 'Actinidia19320' => 'ach', 'Actinidia33068' => 'ach', 'Actinidia35745' => 'ach', 'Ah.02g110500' => 'amhyb', 'Ah.03g132730' => 'amhyb', 'Ah.11g051620' => 'amhyb', 'AL1G37460' => 'aly', 'AL2G29790' => 'aly', 'AL5G17370' => 'aly', 'AL8G39740' => 'aly', 'Aqoxy3G01035' => 'aox', 'Aqoxy3G02945' => 'aox', 'Aqoxy478s001' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0Y9TID' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1F4WXR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24GIPR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.37H86D' => 'arhy', 'AT1G23710' => 'ath', 'AT1G70420' => 'ath', 'AT3G27880' => 'ath', 'AT5G62770' => 'ath', 'ATR0730G039' => 'atr', 'Atru.chr11.2037' => 'acertr', 'Atru.chr6.2310' => 'acertr', 'Atru.chr9.2477' => 'acertr', 'AUR62005386' => 'cqu', 'BcaB02g09692' => 'bca', 'BcaB03g14139' => 'bca', 'BcaB03g14799' => 'bca', 'BcaB03g14801' => 'bca', 'BcaB05g24567' => 'bca', 'BcaB06g27478' => 'bca', 'BcaB07g30140' => 'bca', 'BcaB07g32354' => 'bca', 'BcaC01g02520' => 'bca', 'BcaC01g02521' => 'bca', 'BcaC03g15182' => 'bca', 'BcaC03g17493' => 'bca', 'BcaC04g23394' => 'bca', 'BcaC06g30955' => 'bca', 'BcaC06g33776' => 'bca', 'BcaC06g35049' => 'bca', 'BcaC08g46484' => 'bca', 'BcaNung01382' => 'bca', 'BcaNung06891' => 'bca', 'BolC2t08816H' => 'bol', 'BolC2t11514H' => 'bol', 'BolC2t11519H' => 'bol', 'BolC3t18649H' => 'bol', 'BolC4t26298H' => 'bol', 'BolC5t30991H' => 'bol', 'BolC6t39498H' => 'bol', 'BolC7t42552H' => 'bol', 'BolC7t44217H' => 'bol', 'BolC9t53796H' => 'bol', 'BraA02t06709Z' => 'bra', 'BraA02t08569Z' => 'bra', 'BraA04t16985Z' => 'bra', 'BraA06t25901Z' => 'bra', 'BraA06t27004Z' => 'bra', 'BraA07t31246Z' => 'bra', 'BraA09t36435Z' => 'bra', 'BraA09t39602Z' => 'bra', 'C02p27600' => 'bna', 'C02p54510' => 'bna', 'C03p63950' => 'bna', 'C04p47030' => 'bna', 'C05p22910' => 'bna', 'C06p44280' => 'bna', 'C07p20310' => 'bna', 'C07p20320' => 'bna', 'C07p37050' => 'bna', 'C09p08840' => 'bna', 'CAN.G206.25' => 'can', 'CAN.G300.10' => 'can', 'CAN.G464.40' => 'can', 'CAN.G464.41' => 'can', 'CAN.G4822.1' => 'can', 'CAN.G628.80' => 'can', 'CAN.G781.10' => 'can', 'CANSAT01G0717' => 'cansat', 'CANSAT64G1643' => 'cansat', 'CANSAT80G2338' => 'cansat', 'CARHR024110' => 'chi', 'CARHR063590' => 'chi', 'CARHR149390' => 'chi', 'CARHR261760' => 'chi', 'CARHR276560' => 'chi', 'Carub.0001s2323' => 'cru', 'Carub.0002s1711' => 'cru', 'Carub.0005s0643' => 'cru', 'Carub.0007s3529' => 'cru', 'Carub.0008s2350' => 'cru', 'Ca_03154_v3' => 'car', 'Ca_04190_v3' => 'car', 'Ca_16179_v3' => 'car', 'Ca_16180_v3' => 'car', 'Ca_21918_v3' => 'car', 'Cc04_g14080' => 'ccan', 'Cc07_g02140' => 'ccan', 'Cc11_g15210' => 'ccan', 'CDE02G0911' => 'cde', 'CDE02G3744' => 'cde', 'CDE06G0264' => 'cde', 'CDE06G0711' => 'cde', 'CDE06G2795' => 'cde', 'CDE07G0471' => 'cde', 'Cfa003475' => 'cfa', 'Cfa009151' => 'cfa', 'Cfa019132' => 'cfa', 'Ciclev10015945m.g' => 'ccl', 'Ciclev10021025m.g' => 'ccl', 'Ciclev10032350m.g' => 'ccl', 'CiPaw.03G039000' => 'cil', 'CiPaw.04G025400' => 'cil', 'CiPaw.05G151600' => 'cil', 'CiPaw.06G071600' => 'cil', 'CiPaw.11G026300' => 'cil', 'CiPaw.12G026500' => 'cil', 'ClCG01G013130' => 'cla', 'ClCG05G025340' => 'cla', 'ClCG06G017020' => 'cla', 'ClCG08G018030' => 'cla', 'ClCG09G018990' => 'cla', 'ClCG10G014180' => 'cla', 'COL.COLO4_30037' => 'col', 'Cpa.g.sc215.13' => 'cpa', 'Cpa.g.sc69.47' => 'cpa', 'Cpa.g.sc76.61' => 'cpa', 'CsaV3_1G001490' => 'csa', 'CsaV3_1G008460' => 'csa', 'CsaV3_3G025060' => 'csa', 'CsaV3_3G042470' => 'csa', 'CsaV3_5G027360' => 'csa', 'CsaV3_5G031560' => 'csa', 'CSS0012689' => 'camsi', 'CSS0035264' => 'camsi', 'CSS0041124' => 'camsi', 'CSS0041696' => 'camsi', 'DCAR_007087' => 'dca', 'DCAR_015048' => 'dca', 'DCAR_016484' => 'dca', 'DCAR_021569' => 'dca', 'DCAR_021689' => 'dca', 'DCAR_024458' => 'dca', 'DCAR_026134' => 'dca', 'DCAR_031106' => 'dca', 'DCAR_031107' => 'dca', 'Dinv00507' => 'din', 'Dinv02893' => 'din', 'Dinv15287' => 'din', 'Dinv18850' => 'din', 'Dinv20655' => 'din', 'Dinv20745' => 'din', 'Dinv24843' => 'din', 'Dinv28326' => 'din', 'Dinv33484' => 'din', 'Duzib068G0287' => 'dzi', 'Duzib147G1636' => 'dzi', 'Duzib187G0831' => 'dzi', 'Duzib205G1255' => 'dzi', 'Duzib251G0551' => 'dzi', 'Duzib264G1045' => 'dzi', 'Duzib268G1217' => 'dzi', 'ECA232G2259' => 'eca', 'ECA232G2759' => 'eca', 'ECA232G3488' => 'eca', 'ECA233G1824' => 'eca', 'ECA234G1455' => 'eca', 'ECA246G0343' => 'eca', 'ECA246G2074' => 'eca', 'ECA246G2993' => 'eca', 'ECA246G3140' => 'eca', 'ECA246G4016' => 'eca', 'ECA247G1054' => 'eca', 'EL10Ac5g10747' => 'bvu', 'EL10Ac6g13679' => 'bvu', 'Eucgr.B00315' => 'egr', 'Eucgr.B03318' => 'egr', 'Eucgr.I01788' => 'egr', 'Eucgr.K02843' => 'egr', 'FAN02G0682' => 'fan', 'FAN04G3199' => 'fan', 'FAN05G2415' => 'fan', 'FAN07G0616' => 'fan', 'FAN08G1819' => 'fan', 'FAN09G0168' => 'fan', 'FAN09G3281' => 'fan', 'FAN12G3240' => 'fan', 'FAN13G1071' => 'fan', 'FAN14G5221' => 'fan', 'FAN17G1475' => 'fan', 'FAN18G1119' => 'fan', 'FAN18G2882' => 'fan', 'FAN22G0614' => 'fan', 'FvH4_4g34370' => 'fve', 'FvH4_5g05310' => 'fve', 'FvH4_6g50800' => 'fve', 'Glyma.01G030300' => 'gma', 'Glyma.02G035200' => 'gma', 'Glyma.04G183300' => 'gma', 'Glyma.05G007000' => 'gma', 'Glyma.05G037600' => 'gma', 'Glyma.06G182500' => 'gma', 'Glyma.08G286400' => 'gma', 'Glyma.16G073400' => 'gma', 'Glyma.17G089500' => 'gma', 'Glyma.19G007600' => 'gma', 'Glyma.19G065000' => 'gma', 'Gohir.A03G139100' => 'ghi', 'Gohir.A04G135400' => 'ghi', 'Gohir.A07G221000' => 'ghi', 'Gohir.A10G103400' => 'ghi', 'Gohir.D02G162000' => 'ghi', 'Gohir.D04G178500' => 'ghi', 'Gohir.D07G227700' => 'ghi', 'Gohir.D10G087500' => 'ghi', 'Gorai.001G262600' => 'gra', 'Gorai.005G182000' => 'gra', 'Gorai.011G095800' => 'gra', 'Gorai.012G171600' => 'gra', 'GSVIVG01032463001' => 'vvi', 'HanXRQChr05g0156231' => 'han', 'HanXRQChr07g0198761' => 'han', 'HanXRQChr08g0208741' => 'han', 'HanXRQChr09g0272191' => 'han', 'HanXRQChr12g0371481' => 'han', 'HanXRQChr14g0450341' => 'han', 'HanXRQChr15g0474571' => 'han', 'HanXRQChr16g0517331' => 'han', 'HanXRQChr17g0547951' => 'han', 'Haze_07471' => 'cav', 'Haze_14681' => 'cav', 'Hma1.2p1_0176F.1_g077400' => 'hma', 'Hma1.2p1_0536F.1_g174000' => 'hma', 'HPP92_004863' => 'vpl', 'HPP92_008301' => 'vpl', 'HPP92_011612' => 'vpl', 'HPP92_020279' => 'vpl', 'HPP92_021340' => 'vpl', 'HPP92_021832' => 'vpl', 'HPP92_023402' => 'vpl', 'HPP92_024719' => 'vpl', 'Lalb_Chr05g0216861' => 'lal', 'Lalb_Chr06g0176001' => 'lal', 'Lalb_Chr07g0182741' => 'lal', 'Lalb_Chr09g0326361' => 'lal', 'Lalb_Chr10g0093891' => 'lal', 'Lalb_Chr13g0297801' => 'lal', 'Lalb_Chr16g0382251' => 'lal', 'Lalb_Chr16g0387341' => 'lal', 'Lalb_Chr21g0319491' => 'lal', 'Lalb_Chr23g0273221' => 'lal', 'Lj1g0001599' => 'lja', 'Lj1g0001602' => 'lja', 'Lj2g0006071' => 'lja', 'Lj2g0013279' => 'lja', 'Lj2g0017957' => 'lja', 'Lj3P1053T32' => 'lonja', 'Lj4g0002962' => 'lja', 'Lj5P124T59' => 'lonja', 'Lj6P806T43' => 'lonja', 'Lj7P592T34' => 'lonja', 'Lj9P449T21' => 'lonja', 'Lju41C35T12' => 'lonja', 'Lsat_1_v5_gn_0_13280' => 'lsa', 'Lsat_1_v5_gn_0_13340' => 'lsa', 'Lsat_1_v5_gn_0_13361' => 'lsa', 'Lsat_1_v5_gn_0_14901' => 'lsa', 'Lsat_1_v5_gn_0_15001' => 'lsa', 'Lsat_1_v5_gn_0_15021' => 'lsa', 'Lsat_1_v5_gn_0_15161' => 'lsa', 'Lsat_1_v5_gn_1_27041' => 'lsa', 'Lsat_1_v5_gn_2_91940' => 'lsa', 'Lsat_1_v5_gn_4_10481' => 'lsa', 'Lsat_1_v5_gn_4_182581' => 'lsa', 'Lsat_1_v5_gn_4_182601' => 'lsa', 'Lsat_1_v5_gn_4_5640' => 'lsa', 'Lsat_1_v5_gn_4_75241' => 'lsa', 'Lsat_1_v5_gn_5_119201' => 'lsa', 'Lsat_1_v5_gn_5_14521' => 'lsa', 'Lsat_1_v5_gn_5_152780' => 'lsa', 'Lsat_1_v5_gn_7_34940' => 'lsa', 'Lsat_1_v5_gn_8_156720' => 'lsa', 'Lsat_1_v5_gn_8_82121' => 'lsa', 'Lsat_1_v5_gn_9_123200' => 'lsa', 'Lsat_1_v5_gn_9_6381' => 'lsa', 'Manes.06G104800' => 'mes', 'Manes.12G028200' => 'mes', 'Manes.13G029800' => 'mes', 'Manes.14G065800' => 'mes', 'Manes.15G167300' => 'mes', 'Manes.17G116400' => 'mes', 'MBI10_g14555_MAGBIO' => 'mbi', 'MBI10_g41913_MAGBIO' => 'mbi', 'MBI16_g32208_MAGBIO' => 'mbi', 'MD09G1032200' => 'mdo', 'MD13G1092700' => 'mdo', 'MD14G1180400' => 'mdo', 'MD16G1093500' => 'mdo', 'Medtr3g077890' => 'mtr', 'Medtr4g105750' => 'mtr', 'Medtr5g034230' => 'mtr', 'Medtr6g006930' => 'mtr', 'Medtr6g006950' => 'mtr', 'Medtr8g064640' => 'mtr', 'Medtr8g064650' => 'mtr', 'MELO3C002262.2' => 'cme', 'MELO3C009961.2' => 'cme', 'MELO3C011996.2' => 'cme', 'MELO3C012966.2' => 'cme', 'MELO3C021548.2' => 'cme', 'MELO3C026293.2' => 'cme', 'MELO3C028098.2' => 'cme', 'Migut.D01930' => 'egut', 'Migut.E00167' => 'egut', 'Migut.H00111' => 'egut', 'Migut.I00012' => 'egut', 'Migut.K01372' => 'egut', 'Migut.L01424' => 'egut', 'MSTRG.11451' => 'ama', 'MSTRG.13369' => 'ama', 'MSTRG.15514' => 'ama', 'MSTRG.23129' => 'ama', 'MSTRG.2399' => 'ama', 'MSTRG.24021' => 'ama', 'MSTRG.3168' => 'ama', 'MSTRG.3297' => 'ama', 'MSTRG.4373' => 'ama', 'MSTRG.7903' => 'ama', 'Nitab4.5_0000031g0470' => 'nta', 'Nitab4.5_0000203g0250' => 'nta', 'Nitab4.5_0000884g0090' => 'nta', 'Nitab4.5_0001017g0090' => 'nta', 'Nitab4.5_0001483g0080' => 'nta', 'Nitab4.5_0004348g0010' => 'nta', 'Nitab4.5_0006281g0050' => 'nta', 'Nitab4.5_0007208g0010' => 'nta', 'Nitab4.5_0007719g0040' => 'nta', 'Nitab4.5_0009783g0040' => 'nta', 'Nn3g21687' => 'nnu', 'Nn4g22768' => 'nnu', 'Oeu003459.1' => 'oeu', 'Oeu016383.1' => 'oeu', 'Oeu022162.1' => 'oeu', 'Oeu037698.1' => 'oeu', 'Oeu037699.1' => 'oeu', 'Oeu040830.1' => 'oeu', 'Oeu040831.1' => 'oeu', 'Oeu043052.2' => 'oeu', 'Oeu048646.1' => 'oeu', 'Oeu054059.1' => 'oeu', 'Oeu055453.1' => 'oeu', 'Oeu056731.1' => 'oeu', 'Oeu060136.1' => 'oeu', 'Oeu062980.1' => 'oeu', 'Oeu062983.1' => 'oeu', 'Os01g0639600' => 'osa', 'Os02g0134200' => 'osa', 'Os05g0568600' => 'osa', 'Os05g0568800' => 'osa', 'Os05g0578100' => 'osa', 'Peaxi162Scf00017g02910' => 'pax', 'Peaxi162Scf00129g00116' => 'pax', 'Peaxi162Scf00700g00055' => 'pax', 'Peaxi162Scf00700g00061' => 'pax', 'Peaxi162Scf00700g00062' => 'pax', 'Peaxi162Scf00700g00066' => 'pax', 'Peaxi162Scf00710g00051' => 'pax', 'PGR044G0982' => 'pgr', 'PGR083G0859' => 'pgr', 'PGR102G1462' => 'pgr', 'PGR119G0161' => 'pgr', 'PGR142G1453' => 'pgr', 'PGSC0003DMG400000492' => 'stu', 'PGSC0003DMG400003250' => 'stu', 'PGSC0003DMG400013482' => 'stu', 'PGSC0003DMG400024504' => 'stu', 'PGSC0003DMG400030091' => 'stu', 'PGSC0003DMG400030093' => 'stu', 'PGSC0003DMG400045223' => 'stu', 'Phvul.002G071000' => 'pvu', 'Phvul.003G060800' => 'pvu', 'Phvul.003G200400' => 'pvu', 'Phvul.004G013400' => 'pvu', 'Phvul.008G155400' => 'pvu', 'Phvul.009G178600' => 'pvu', 'Potri.008G156901' => 'ptr', 'Potri.009G102101' => 'ptr', 'Potri.010G041300' => 'ptr', 'Potri.012G081000' => 'ptr', 'Potri.015G076400' => 'ptr', 'Potri.018G096400' => 'ptr', 'Potri.018G096600' => 'ptr', 'Prupe.1G253100' => 'ppe', 'Prupe.3G285800' => 'ppe', 'Prupe.5G173800' => 'ppe', 'Psat0s603g0120' => 'psa', 'Psat1g057280' => 'psa', 'Psat1g057320' => 'psa', 'Psat1g057400' => 'psa', 'Psat1g058560' => 'psa', 'Psat2g104240' => 'psa', 'Psat4g058040' => 'psa', 'Psat4g123640' => 'psa', 'Psat4g123680' => 'psa', 'Psat5g114600' => 'psa', 'Psat5g224520' => 'psa', 'PSO210G3280' => 'pso', 'PSO339G3614' => 'pso', 'PSO384G1089' => 'pso', 'PSO732G0803' => 'pso', 'QL01p007608' => 'qlo', 'QL02p076295' => 'qlo', 'QL03p060170' => 'qlo', 'QL04p042273' => 'qlo', 'QL10p011670' => 'qlo', 'RcHm_v2.0_Chr2g0172191' => 'rch', 'RcHm_v2.0_Chr4g0443781' => 'rch', 'RcHm_v2.0_Chr7g0193551' => 'rch', 'Rhsim08G0053900' => 'rsi', 'Rhsim08G0054000' => 'rsi', 'Rhsim08G0054200' => 'rsi', 'Rhsim08G0054300' => 'rsi', 'Rhsim08G0172000' => 'rsi', 'Rhsim10G0021000' => 'rsi', 'Rhsim12G0045800' => 'rsi', 'Rhsim12G0118800' => 'rsi', 'Sabra10G0026000' => 'sbr', 'Sabra12G0057900' => 'sbr', 'Sabra15G0101500' => 'sbr', 'Sabra18G0083800' => 'sbr', 'SalBow1G0495' => 'sbo', 'SalBow2G0497' => 'sbo', 'SalBow2G2010' => 'sbo', 'SalBow5G0542' => 'sbo', 'SalBow5G1950' => 'sbo', 'SalBow7G3341' => 'sbo', 'SalBow8G3931' => 'sbo', 'Sc04g0001810' => 'sci', 'Sc04g0009180' => 'sci', 'Sc07g0003050' => 'sci', 'Sc16g0003590' => 'sci', 'Sed0001479' => 'sed', 'Sed0011194' => 'sed', 'Sed0011422' => 'sed', 'Sed0011915' => 'sed', 'Sed0020184' => 'sed', 'Sed0026383' => 'sed', 'Sed0026640' => 'sed', 'Sed0027867' => 'sed', 'SGA_v2.0_scaffold114G31836' => 'sas', 'SGA_v2.0_scaffold135G34879' => 'sas', 'SGA_v2.0_scaffold165G38234' => 'sas', 'SGA_v2.0_scaffold205G41690' => 'sas', 'SGA_v2.0_scaffold224G42977' => 'sas', 'SGA_v2.0_scaffold25G10842' => 'sas', 'SGA_v2.0_scaffold30G12462' => 'sas', 'SGA_v2.0_scaffold63G21699' => 'sas', 'SGA_v2.0_scaffold7G04133' => 'sas', 'SGA_v2.0_scaffold8G04207' => 'sas', 'SGA_v2.0_scaffold90G27938' => 'sas', 'Solyc02g086810.1' => 'sly', 'Solyc03g114350.1' => 'sly', 'Solyc04g024780.1' => 'sly', 'Solyc04g028460.1' => 'sly', 'Solyc05g005260.3' => 'sly', 'Solyc12g062160.1' => 'sly', 'Solyc12g062170.1' => 'sly', 'Solyc12g062220.1' => 'sly', 'Sopen02g031580' => 'spe', 'Sopen03g033450' => 'spe', 'Sopen04g010680' => 'spe', 'Sopen05g001270' => 'spe', 'Sopen06g027760' => 'spe', 'Sopen12g024590' => 'spe', 'Sopen12g024750' => 'spe', 'Sp1g21110' => 'spa', 'Sp2g16940' => 'spa', 'Sp2g25940' => 'spa', 'Sp5g25500' => 'spa', 'Sp7g01610' => 'spa', 'TAR371G1086' => 'tar', 'TAR622G0132' => 'tar', 'TAR629G2362' => 'tar', 'THA.LOC104818236' => 'tha', 'THA.LOC104821458' => 'tha', 'THA.LOC104822146' => 'tha', 'THA.LOC104823942' => 'tha', 'THA.LOC104824695' => 'tha', 'THA.LOC104825335' => 'tha', 'Thecc.02G251000' => 'tca', 'Thecc.03G012600' => 'tca', 'Thecc.04G010500' => 'tca', 'Thhalv10004779m.g' => 'esa', 'Thhalv10005715m.g' => 'esa', 'Thhalv10008273m.g' => 'esa', 'Thhalv10018979m.g' => 'esa', 'Thhalv10027885m.g' => 'esa', 'TPR.G11715' => 'tpr', 'TPR.G11745' => 'tpr', 'TPR.G1693' => 'tpr', 'TPR.G21083' => 'tpr', 'TPR.G2264' => 'tpr', 'TPR.G37511' => 'tpr', 'TWI18G0496' => 'twi', 'TWI23G0219' => 'twi', 'TWI31G0459' => 'twi', 'TWI36G0293' => 'twi', 'TWI36G1740' => 'twi', 'TWI39G0739' => 'twi', 'TWI56G0447' => 'twi', 'unitig_22.g6937' => 'ugi', 'unitig_26.g10361' => 'ugi', 'unitig_26.g8800' => 'ugi', 'unitig_37.g12427' => 'ugi', 'unitig_46.g18708' => 'ugi', 'unitig_699.g19938' => 'ugi', 'unitig_749.g13278' => 'ugi', 'unitig_750.g28471' => 'ugi', 'vmacro01168' => 'vma', 'vmacro18253' => 'vma', 'vmacro18254' => 'vma', 'vmacro18255' => 'vma', 'VMungo0251G0973' => 'vmu', 'VMungo0464G0972' => 'vmu', 'VMungo1215G0354' => 'vmu', 'VMungo1215G2839' => 'vmu', 'VMungo1309G2238' => 'vmu', 'VMungo1383G2935' => 'vmu', 'Zm00001eb157710' => 'zma', 'Zm00001eb158820' => 'zma', 'Zm00001eb209140' => 'zma', 'Zm00001eb296270' => 'zma', 'Zm00001eb296280' => 'zma', 'Zm00001eb296760' => 'zma', 'Zm00001eb344100' => 'zma', 'Zm00001eb359160' => 'zma' ) $gf_id = 'HOM05D001111' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001111' ) $data_identifier = 'HOM05D001111' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 4, 'ath' => (int) 4, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 19, 'bol' => (int) 10, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 6, 'col' => (int) 1, 'cpa' => (int) 3, 'csa' => (int) 6, 'camsi' => (int) 4, 'dca' => (int) 9, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 11, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 1, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 8, 'lal' => (int) 10, 'lja' => (int) 6, 'lonja' => (int) 6, 'lsa' => (int) 22, 'mes' => (int) 6, 'mbi' => (int) 3, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 7, 'egut' => (int) 6, 'ama' => (int) 10, 'nta' => (int) 10, 'nnu' => (int) 2, 'oeu' => (int) 15, 'osa' => (int) 5, 'pax' => (int) 7, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 7, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 7, 'sci' => (int) 4, 'sed' => (int) 8, 'sas' => (int) 11, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 3, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 8, 'vma' => (int) 4, 'vmu' => (int) 6, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb359160' $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